Fix apt command in CI

cfe-lab · Dec 6, 2024 · 740c11a · 740c11a
1 parent 8dc4a23
commit 740c11a
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diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
@@ -17,7 +17,7 @@ jobs:
 
       - name: Installing blast
         run: |
-          sudo apt-get install -q -y ncbi-blast+
+          sudo apt-get install -qq ncbi-blast+
 
       - name: Install Haploflow
         run: |

diff --git a/Dockerfile b/Dockerfile
@@ -45,8 +45,8 @@ RUN wget -qO rustup.sh https://sh.rustup.rs && \
     cargo install --root / --git https://github.com/jeff-k/merge-mates.git --rev 2fec61363f645e2008a4adff553d098beae21469
 
 ## Installing blast
-RUN apt-get install -q -y ncbi-blast+ && \
-    rm -rf /var/lib/apt/lists/*
+RUN apt-get update -qq --fix-missing && \
+    apt-get install -q -y ncbi-blast+
 
 ## bowtie2
 RUN wget -q -O bowtie2.zip https://github.com/BenLangmead/bowtie2/releases/download/v2.2.8/bowtie2-2.2.8-linux-x86_64.zip && \